Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_232502519.1 LFE_RS09120 ATP-binding cassette domain-containing protein
Query= TCDB::G3LHY8 (358 letters) >NCBI__GCF_000284315.1:WP_232502519.1 Length = 588 Score = 91.3 bits (225), Expect = 6e-23 Identities = 70/205 (34%), Positives = 106/205 (51%), Gaps = 9/205 (4%) Query: 24 LERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFDGTDVTGMPVQKR-NVAMVYQQF 82 L++G++ L+GP AGKT+LMRL++GL P GG I G D + P+ + ++ + Q+F Sbjct: 37 LKKGSITGLIGPDGAGKTTLMRLLSGLLWPDGGDIRIMGNDPSKAPLSVQGSLGYMPQKF 96 Query: 83 INYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKLT---PYLDRTPLNLSGGQQQR 139 Y L+V N+ + G DR A LL +T P+ R LSGG +Q+ Sbjct: 97 GLYEDLSVQENLDLYANLQGVPK---DRRKELYAPLLSMTGLSPFQKRLAGQLSGGMKQK 153 Query: 140 TALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQSGAIFVYATTEPSEALLLG 199 +A +LV ++L+DEP +D R EL E L K+ ++SGA +T+ EA Sbjct: 154 LGVACSLVHQPPILLLDEPTVGVDPVSRRELWEILRKLVSESGATLFVSTSYLDEAERC- 212 Query: 200 GNTATLNQGRVTQFGPTIEVYRRPV 224 L G+V GP E +R+ V Sbjct: 213 DEILILYNGKVLGSGPP-ESFRKEV 236 Score = 73.2 bits (178), Expect = 2e-17 Identities = 46/147 (31%), Positives = 75/147 (51%), Gaps = 1/147 (0%) Query: 24 LERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFDGTDVTGMPVQKRN-VAMVYQQF 82 +++G + LLG AGKT+ R++AGL PT G + G DV + Q R + + Q+F Sbjct: 364 VKKGEVFGLLGANGAGKTTTFRMLAGLLEPTAGKLIVAGEDVRKVAAQARGKIGYMAQKF 423 Query: 83 INYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKLTPYLDRTPLNLSGGQQQRTAL 142 Y LTV+ N+ G +++ + +L PY + + L G +QR AL Sbjct: 424 SLYSQLTVFQNLIFYSSAYGLSGTLQKEKIQDSLNFFELEPYKNVSSGILPLGFRQRLAL 483 Query: 143 ARALVKNASLVLMDEPLANLDYKLREE 169 + AL+ S++ +DEP + +D R E Sbjct: 484 SCALIHEPSILFLDEPTSGVDPNARRE 510 Lambda K H 0.319 0.136 0.392 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 495 Number of extensions: 28 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 358 Length of database: 588 Length adjustment: 33 Effective length of query: 325 Effective length of database: 555 Effective search space: 180375 Effective search space used: 180375 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory